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The 4D scanning transmission electron microscopy (STEM) method has enabled mapping of the structure and functionality of solids on the atomic scale, yielding information-rich data sets containing information on the interatomic electric and magnetic fields, structural and electronic order parameters, and other symmetry breaking distortions. A critical bottleneck on the pathway toward harnessing 4D-STEM for materials exploration is the dearth of analytical tools that can reduce complex 4D-STEM data sets to physically relevant descriptors. Classical machine learning (ML) methods such as principal component analysis and other linear unmixing techniques are limited by the presence of multiple point-group symmetric variants, where diffractograms from each rotationally equivalent position will form its own component. This limitation even holds for more complex ML methods, such as convolutional neural networks. Here, we propose and implement an approach for the systematic exploration of symmetry breaking phenomena from 4D-STEM data sets using rotationally invariant variational autoencoders (rrVAE), which is designed to disentangle the general rotation of the object from other latent representations. The implementation of purely rotational rrVAE is discussed as are applications to simulated data for graphene and zincblende structures that illustrate the effect of site symmetry breaking. Finally, the rrVAE analysis of 4D-STEM data of vacancies in graphene is illustrated and compared to the classical center-of-mass (COM) analysis. This approach is universal for probing of symmetry breaking phenomena in complex systems and can be implemented for a broad range of diffraction methods exploring the 2D diffraction space of the system, including X-ray ptychography, electron backscatter diffraction (EBSD), and more complex methods.